Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010005.1 Kokia drynarioides strain JFW-HI SEQ_124764, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 84986
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:976 original size:23 final size:23
Alignment explanation
Indices: 950--1074 Score: 126
Period size: 23 Copynumber: 5.3 Consensus size: 23
940 ACACTAGCAC
950 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * * *
973 GCTCTTTGTTTAGCAC-GTTTTTT
1 GCTCTCTGATTAGCACTG-TGTGT
996 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
* *
1021 GCTCTCTGATTAGCATTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
1044 GCTCTCTGACTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
1067 ACTCTCTG
1 GCTCTCTG
1075 TTGCCCAGCA
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.01
23 64 0.76
25 18 0.21
26 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.46
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:1019 original size:48 final size:46
Alignment explanation
Indices: 950--1074 Score: 146
Period size: 48 Copynumber: 2.7 Consensus size: 46
940 ACACTAGCAC
* *
950 GCTCTCTGATTAGCACTGTGTGTGCTCTTTGTTTAGCACGTTTT-T-T
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCA--TTTTGTGT
996 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCATTTTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCATTTTGTGT
* * * *
1044 GCTCTCTGACTAGTACTTTGTGTACTCTCTG
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTG
1075 TTGCCCAGCA
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
46 31 0.45
47 1 0.01
48 37 0.54
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.46
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCATTTTGTGT
Found at i:3269 original size:24 final size:24
Alignment explanation
Indices: 3241--3291 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
3231 AATTTGACTC
*
3241 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
3265 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
3289 AAA
1 AAA
3292 GATTATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:3394 original size:24 final size:24
Alignment explanation
Indices: 3366--3416 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3356 AATTGGACTC
* *
3366 AAACAAATAAACAGTGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
*
3390 AAACAAATAAGCAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
3414 AAA
1 AAA
3417 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.10, G:0.14, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:3433 original size:125 final size:125
Alignment explanation
Indices: 3211--3589 Score: 686
Period size: 125 Copynumber: 3.0 Consensus size: 125
3201 AATAATAATA
*
3211 AAATAATCTAGACTAATAAGAATTTGACTCAAACAAATAAACAGAGTTTAATTGAAACAAATAAA
1 AAATAATCTAGAGTAATAAGAATTTGACTCAAACAAATAAACAGAGTTTAATTGAAACAAATAAA
3276 CAGAGTTTAACTGAAAGATTATTTCTCAAATTTGACTTGAAATAGGAGTCATAATTCAAC
66 CAGAGTTTAACTGAAAGATTATTTCTCAAATTTGACTTGAAATAGGAGTCATAATTCAAC
* * *
3336 AAATAATCTAGAGTAATAAGAATTGGACTCAAACAAATAAACAGTGTTTAATTGAAACAAATAAG
1 AAATAATCTAGAGTAATAAGAATTTGACTCAAACAAATAAACAGAGTTTAATTGAAACAAATAAA
*
3401 CAGAGTTTAACTGAAAGATTATTTCTCAAATTTGACTTGAAATAGGAGTCATAATTTAAC
66 CAGAGTTTAACTGAAAGATTATTTCTCAAATTTGACTTGAAATAGGAGTCATAATTCAAC
*
3461 AAATAATCTAAAGTAATAAGAATTTGACTCAAACAAATAAACAGAGTTTAATTGAAACAAATAAA
1 AAATAATCTAGAGTAATAAGAATTTGACTCAAACAAATAAACAGAGTTTAATTGAAACAAATAAA
* *
3526 CAGAGTTTAACTGAAAGATTATTTCTCAAATTTGACTTGAAATAAGAGTTATAATTCAAC
66 CAGAGTTTAACTGAAAGATTATTTCTCAAATTTGACTTGAAATAGGAGTCATAATTCAAC
3586 AAAT
1 AAAT
3590 CTCCACCTTG
Statistics
Matches: 242, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
125 242 1.00
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.29
Consensus pattern (125 bp):
AAATAATCTAGAGTAATAAGAATTTGACTCAAACAAATAAACAGAGTTTAATTGAAACAAATAAA
CAGAGTTTAACTGAAAGATTATTTCTCAAATTTGACTTGAAATAGGAGTCATAATTCAAC
Found at i:3519 original size:24 final size:24
Alignment explanation
Indices: 3491--3541 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
3481 AATTTGACTC
*
3491 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
3515 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
3539 AAA
1 AAA
3542 GATTATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:5547 original size:24 final size:24
Alignment explanation
Indices: 5481--5555 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
5471 AATTTAACTC
* * *
5481 AAACAACTAAACAAAGTTTAATTG
1 AAACAAATAAAGAGAGTTTAATTG
*
5505 AAATAAATAAAGAGAGTTTAATTG
1 AAACAAATAAAGAGAGTTTAATTG
* *
5529 AAACAAAT-AAGCAGGGTTTAACTG
1 AAACAAATAAAG-AGAGTTTAATTG
5553 AAA
1 AAA
5556 GATTATTTCT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 3 0.07
24 40 0.93
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.24
Consensus pattern (24 bp):
AAACAAATAAAGAGAGTTTAATTG
Found at i:16905 original size:43 final size:43
Alignment explanation
Indices: 16857--16943 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 43
16847 TTAATCACCT
*
16857 TAATTGTTTC-TTTTCAATTTAATCAAACTTTA-AATATTCTCAC
1 TAATTGTTTCATTTT-AATTTAATC-AACTTTATAATATGCTCAC
*
16900 TAATTGTTTCATTTTAATTTAATCTACTTTATAATATGCTCAC
1 TAATTGTTTCATTTTAATTTAATCAACTTTATAATATGCTCAC
16943 T
1 T
16944 TAAACCGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
42 6 0.15
43 30 0.75
44 4 0.10
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (43 bp):
TAATTGTTTCATTTTAATTTAATCAACTTTATAATATGCTCAC
Found at i:20388 original size:21 final size:21
Alignment explanation
Indices: 20306--20394 Score: 86
Period size: 21 Copynumber: 4.6 Consensus size: 21
20296 GTCGTCCCAA
20306 AAATCGATTGTTTATATGTTT
1 AAATCGATTGTTTATATGTTT
** *
20327 AAATTTATTG-TTATA-GTGT
1 AAATCGATTGTTTATATGTTT
*
20346 -AAT--ACTGTTTAT-T-TTT
1 AAATCGATTGTTTATATGTTT
20362 -AATCGATTGTTTATATGTTT
1 AAATCGATTGTTTATATGTTT
20382 AAATCGATTGTTT
1 AAATCGATTGTTT
20395 TATAACATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
16 8 0.15
17 4 0.07
18 11 0.20
19 4 0.07
20 8 0.15
21 20 0.36
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.54
Consensus pattern (21 bp):
AAATCGATTGTTTATATGTTT
Found at i:25008 original size:30 final size:30
Alignment explanation
Indices: 24967--25033 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
24957 ACAACAAGAG
* * *
24967 GACTATTTTGTCAC-TTTCGATAACTTTAGT
1 GACTGTTTTGTCACATTTCCA-AACTTGAGT
*
24997 GACTGTTTTGTCACATTTCCAAAGTTGAGT
1 GACTGTTTTGTCACATTTCCAAACTTGAGT
25027 GACTGTT
1 GACTGTT
25034 GTGTTAAACG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.43
Consensus pattern (30 bp):
GACTGTTTTGTCACATTTCCAAACTTGAGT
Found at i:28057 original size:15 final size:14
Alignment explanation
Indices: 28033--28062 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
28023 AAGTGTCAAT
28033 AAATTAAATTAAAA
1 AAATTAAATTAAAA
28047 AAATCTAAATTAAAA
1 AAAT-TAAATTAAAA
28062 A
1 A
28063 TTGTCGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
AAATTAAATTAAAA
Found at i:28823 original size:30 final size:30
Alignment explanation
Indices: 28783--28897 Score: 128
Period size: 30 Copynumber: 3.9 Consensus size: 30
28773 ACATCAAAAC
*
28783 GGGGTCAAATTTTAATTTTT-GAAAACTTTA
1 GGGGTCAAATTTGAATTTTTGGAAAA-TTTA
*
28813 GGGGTTAAATTTGAATTTTTGGAAAATTTA
1 GGGGTCAAATTTGAATTTTTGGAAAATTTA
* * *
28843 GGAGTCAGATTTGAATTTTTGGAAAA-TTC
1 GGGGTCAAATTTGAATTTTTGGAAAATTTA
* *
28872 GAGGGTTAAATTTGAATCTTT-GAAAA
1 G-GGGTCAAATTTGAATTTTTGGAAAA
28898 CTTCGGATGA
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.11
30 60 0.82
31 5 0.07
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (30 bp):
GGGGTCAAATTTGAATTTTTGGAAAATTTA
Found at i:38904 original size:3 final size:3
Alignment explanation
Indices: 38896--38925 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
38886 CCCGCCAGTT
38896 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
38926 GTACGCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:40775 original size:31 final size:32
Alignment explanation
Indices: 40729--40800 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
40719 ATTTTTTTCA
* *
40729 AATTTATTGAAAAATATTTGTTTTAAT-TTTT
1 AATTTATTGAAAAATACTTATTTTAATATTTT
* *
40760 AATTTGTTGAGAAATACTTATTTTAATATTTTT
1 AATTTATTGAAAAATACTTATTTTAATA-TTTT
*
40793 AATGTATT
1 AATTTATT
40801 AGATATATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 23 0.70
33 10 0.30
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.56
Consensus pattern (32 bp):
AATTTATTGAAAAATACTTATTTTAATATTTT
Found at i:52403 original size:2 final size:2
Alignment explanation
Indices: 52396--52450 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
52386 GAAGCAATCT
52396 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52438 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
52451 GACCCTAATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55057 original size:16 final size:18
Alignment explanation
Indices: 55036--55070 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
55026 TTTTACTATC
55036 ATTAATT-TAAAAT-TTT
1 ATTAATTATAAAATATTT
55052 ATTAATTATAAAATATTT
1 ATTAATTATAAAATATTT
55070 A
1 A
55071 AATAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 6 0.35
18 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTAATTATAAAATATTT
Found at i:55065 original size:50 final size:50
Alignment explanation
Indices: 54971--55065 Score: 120
Period size: 51 Copynumber: 1.9 Consensus size: 50
54961 TTTATATATT
* * *
54971 TATAATTTTAAATAATTAAATTAAATTTTTATTATTTTTGAAAATCATAA
1 TATAATTTTAAATAATTAAATTAAAATTTTATTAATTATGAAAATCATAA
* * *
55021 TATAATTTTACTATCATTAATTTAAAATTTTATTAATTAT-AAAAT
1 TATAATTTTA-AATAATTAAATTAAAATTTTATTAATTATGAAAAT
55066 ATTTAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 15 0.39
51 23 0.61
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (50 bp):
TATAATTTTAAATAATTAAATTAAAATTTTATTAATTATGAAAATCATAA
Found at i:59340 original size:23 final size:23
Alignment explanation
Indices: 59298--59341 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
59288 GGAATTGAAG
* * *
59298 AATAATTTTTTGATGGATTAAAA
1 AATAATTTTATAATGCATTAAAA
59321 AATAATTTTATAATGCATTAA
1 AATAATTTTATAATGCATTAA
59342 TCTATGTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (23 bp):
AATAATTTTATAATGCATTAAAA
Found at i:84781 original size:50 final size:53
Alignment explanation
Indices: 84664--84789 Score: 143
Period size: 56 Copynumber: 2.4 Consensus size: 53
84654 CAGAATAGAT
* * *
84664 AAAATTGAATAATTGAATTACTATTTTGTAATTTTTTATAATTGAATGACCAAAA
1 AAAATT-AATAATTGAGTGACTATTTTGTAATTTTTTATAATTAAATGA-CAAAA
*
84719 AAAATACTAATAATTGAGTGACTGTTTTGTAA-TTTTT-TAATTAAAT-A-ATAAA
1 AAAAT--TAATAATTGAGTGACTATTTTGTAATTTTTTATAATTAAATGACA-AAA
84771 AAAATTAATAATTGAGTGA
1 AAAATTAATAATTGAGTGA
84790 TTGTGAGTAG
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
50 14 0.22
51 1 0.02
52 8 0.12
53 1 0.02
54 8 0.12
55 10 0.16
56 21 0.33
57 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.40
Consensus pattern (53 bp):
AAAATTAATAATTGAGTGACTATTTTGTAATTTTTTATAATTAAATGACAAAA
Found at i:84950 original size:2 final size:2
Alignment explanation
Indices: 84945--84974 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
84935 TTTTATTAAC
84945 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
84975 AATACAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.